Genome-wide identification and expression pattern analysis of pseudogenes in Strobilanthes cusia (Nees) Kuntze

Objective Pseudogenes are often referred to as “junk DNA.” Although they have been well characterized in mammals, pseudogenes have been identified in only a few plant species. As an important traditional Chinese medicinal plant, the genome of Strobilanthes cusia (Nees) Kuntze has recently been released, providing a valuable opportunity to explore pseudogenes in S. cusia . Methods Based on the S. cusia genome, pseudogenes were identified using the Soft PseudoPipe tool, and their evolutionary patterns and expression profiles across different tissues and developmental stages were analyzed. Results A total of 3156 pseudogenes were identified. DUP-type pseudogenes exhibited more insertion and frameshift mutations than PSSD-type pseudogenes; furthermore, a recent expansion of DUP-type pseudogenes was observed. Expression analysis detected 802 pseudogenes expressed in various tissues, primarily associated with plant defense functions according to Gene Ontology enrichment analysis. Among these, DUP-type pseudogenes were the most prevalent, with most arising recently. Additionally, 45 pseudogenes corresponding to gene family members involved in the biosynthesis of the medicinal compounds (indigo and indirubin) in S. cusia were identified, of which 27 were expressed in different tissues. Conclusions In this study, we successfully identified and characterized 3156 pseudogenes in S. cusia . Additionally, we analyzed the expression patterns of these pseudogenes. Our findings contribute to a better understanding of pseudogenes in S. cusia .